Only two come to my mind and the second is questionable.
1. That the Honored Matre was the produce of Fish Speakers, wild Reverend Mothers and Tleilaxu females. The later of which is the reason why the HM's Other Memories were blocked to the BG. This was the only moment in all of the new books that made me pause while reading, the only Eureka! moment when the puzzle pieces from HoD and CH:D seemed to fall into place. Of course how it was presented and the fact that the Enemy turned out to be Robots in Space kind of made the idea pointless to their story. But if we ignore what they wrote, which I am sure we all try to do, and think about the story how we think Frank would have written it makes the unwritten story much more interesting. If we assume that the Enemy was Face Dancers, which seems obvious to anyone that read the books, the conflict between the two takes on different dimensions. If we take the fact that the Weapon that the HM stole from the enemy instead of just killing everyone cause them to become brain dead and combine the fact that FD are mules we can come to the conclusion that the FD were using the brain dead female bodies to create Tanks so they can reproduce. This would only have inflamed the HM unconscious genetic memories of their times as tanks.
2. Water Worms. Now I haven't read through Hunters yet only checked the summary on wikipedia, but if we dismiss the idea of Ultra-Spice as it should be (Spice is already the ultimate substance, how can you make it better, does it fly?), the idea of Water Worms has some merit. Now at the end of CH:D we have only one source of spice that which is being produced with the new spice cycle on Chapterhouse. This scenario could create a new hydraulic empire, a turning inward, with the elimination of Rakis and the Tleilaxu source. Now the BG did send out No-Ships in order to start the spice cycle on other planets but I always got the feel from Odrade (I think) that these attempts were in vain. The major issue in establishing the spice cycle seems to be water. Now if a sandtrout/worm could be developed that was resistant to water then the spice cycle could be established on any world. This would mean that it can no longer be controlled, no more monopolies, no more inward turning of humanity. I don't know I am still torn on this idea.
Oh yeah! Who could forget......?
3. The Normacle was the ultimate being who sat around for 20,000 years doing nothing and then swooped in to save the day and made all the previous books pointless

So are there any other ideas that had that Frank feel in the Prequels? If yes what were they and why? And please counter and embellish my ideas above.